Variant report

Variant	rs1582874
Chromosome Location	chr3:141115219-141115220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141110442..141112822-chr3:141113181..141115807,2	MCF-7	breast:
2	chr3:141114089..141115848-chr3:141123999..141126481,2	K562	blood:
3	chr3:141110512..141116314-chr3:141119698..141124103,10	MCF-7	breast:
4	chr3:141114505..141117008-chr3:141133562..141135723,2	K562	blood:
5	chr3:141106542..141109446-chr3:141114949..141116748,2	MCF-7	breast:
6	chr3:141113620..141116005-chr3:141118061..141119671,2	MCF-7	breast:
7	chr3:141102597..141106298-chr3:141113408..141116630,4	MCF-7	breast:
8	chr3:141112658..141115494-chr3:141157644..141160084,2	K562	blood:
9	chr3:141089088..141091263-chr3:141115088..141117204,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13068733	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13077048	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1344672	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1344674	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1346408	0.82[CEU][hapmap]
rs1863868	0.82[CEU][hapmap]
rs1991431	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114867	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2871960	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4683605	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683606	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6440003	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6763927	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6763931	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6764769	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6785012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724016	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7625643	0.87[EUR][1000 genomes]
rs7632381	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7650602	0.87[EUR][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853018	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
2	chr3:141106000-141115400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:141106000-141115800	Weak transcription	Right Ventricle	heart
4	chr3:141106000-141117000	Strong transcription	Fetal Intestine Large	intestine
5	chr3:141106000-141119000	Weak transcription	Colonic Mucosa	Colon
6	chr3:141106800-141119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:141108000-141116000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:141108400-141115400	Weak transcription	Liver	Liver
9	chr3:141108400-141118200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:141108400-141118600	Weak transcription	Small Intestine	intestine
11	chr3:141110400-141118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:141111600-141118000	Weak transcription	Pancreas	Pancrea
13	chr3:141111600-141120800	Weak transcription	Gastric	stomach
14	chr3:141112000-141116600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:141112000-141119000	Weak transcription	Fetal Heart	heart
16	chr3:141112400-141115400	Weak transcription	HMEC	breast
17	chr3:141112400-141116600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr3:141112400-141117000	Strong transcription	A549	lung
19	chr3:141112400-141120000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:141112600-141115400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:141112600-141116000	Weak transcription	HepG2	liver
22	chr3:141112600-141116800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:141112600-141120400	Weak transcription	Fetal Stomach	stomach
24	chr3:141112600-141120600	Weak transcription	Lung	lung
25	chr3:141112800-141115400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:141112800-141115400	Weak transcription	Ovary	ovary
27	chr3:141112800-141115600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141112800-141115800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:141112800-141116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:141112800-141119200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:141112800-141120400	Weak transcription	Hela-S3	cervix
32	chr3:141112800-141120600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:141112800-141120600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:141112800-141120800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:141113200-141117400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:141113200-141119600	Strong transcription	HSMM	muscle
37	chr3:141113400-141115800	Strong transcription	HSMMtube	muscle
38	chr3:141113400-141116800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:141113400-141117000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:141113400-141118200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:141113600-141115600	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:141113600-141115800	Strong transcription	Fetal Lung	lung
43	chr3:141113600-141116000	Strong transcription	Osteobl	bone
44	chr3:141113600-141116800	Strong transcription	K562	blood
45	chr3:141113600-141117400	Strong transcription	Placenta	Placenta
46	chr3:141113800-141115800	Weak transcription	NHLF	lung
47	chr3:141113800-141118600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:141114000-141117400	ZNF genes & repeats	GM12878-XiMat	blood
49	chr3:141114000-141117400	Strong transcription	NH-A	brain
50	chr3:141114000-141118200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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